February 3, 2018

Today’s digest is short, but has exciting reads on how machine learning is improving prediction of antibiotic resistance genes.

General Microbiome

Construction of Effective Minimal Active Microbial Consortia for Lignocellulose Degradation. Puentes-Téllez PE. Microbial Ecology

Review: Role of antimicrobial peptides in controlling symbiotic bacterial populations. Mergaert P. Natural Product Reports

Evaluation of the ability of commercial wine yeasts to form biofilms (mats) and adhere to plastic: implications for the microbiota of the winery environment.Tek EL. FEMS Microbiology Ecology

Gut Microbiome

The mechanistic link between health and gut microbiota diversity.Larsen OFA. Scientific Reports

REVIEW:The Role of Gut Microbiome and Associated Metabolome in the Regulation of Neuroinflammation in Multiple Sclerosis and Its Implications in Attenuating Chronic Inflammation in Other Inflammatory and Autoimmune Disorders.Dopkins N. Immunology

Plant, Soil, and Water Microbiome

Lithobiontic life: “Atacama rocks are well and alive”. Gómez-Silva B.Antonie Van Leeuwenhoek

Contrasting patterns of the bacterial and archaeal communities in a high-elevation river in northwestern China. Hu Y. Journal of Microbiology

Arbuscular Mycorrhizal Fungi and Plant Chemical Defence: Effects of Colonisation on Aboveground and Belowground Metabolomes. Hill EM. Journal of Chemical Ecology

Comparison of plants with C3 and C4 carbon fixation pathways for remediation of polycyclic aromatic hydrocarbon contaminated soils. Sivaram AK. Scientific Reports

Soda pans of the Pannonian steppe harbor unique bacterial communities adapted to multiple extreme conditions. Szabó A. Exremophiles

The effects of glyphosate, glufosinate, paraquat and paraquat-diquat on soil microbial activity and bacterial, archaeal and nematode diversity.Dennis PG. Scientific Reports

Soil commensal rhizobia promote Rhizobium etli nodulation efficiency through CinR-mediated quorum sensing. Miao J. Archives of Microbiology

Distribution of thermophilic endospores in a temperate estuary indicate that dispersal history structures sediment microbial communities.Bell E. Environmental Microbiology

Animal Experiments and Microbiome

Age-associated microbiome shows the giant panda lives on hemicelluloses, not on cellulose. Zhang W. ISME Journal

Increased productivity in poultry birds by sub-lethal dose of antibiotics is arbitrated by selective enrichment of gut microbiota, particularly short-chain fatty acid producers. Banerjee S. Microbiology

Whole metagenome sequencing reveals links between mosquito microbiota and insecticide resistance in malaria vectors. Dada N. Scientific Reports

Virome

The virome of the arbuscular mycorrhizal fungus Gigaspora margarita reveals the first report of DNA fragments corresponding to replicating non-retroviral RNA viruses in Fungi.Turina M. Environmental Microbiology

Techniques/Protocols

DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data.Arango-Argoty G. Microbiome

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January 25, 2018

Female sexual and reproductive microbiome: A Bayesian network of the relationship between the vaginal microbiome, habits, demographics and infection risk in reproductive age women, a new mouse model of HIV co-infection demonstrates increased viral shedding in the vagina after gonorrhoeae bacterial infection, and the impacts of diet-induced obesity during pregnancy on the maternal metabolome and gene expression in the placenta in mice.

Water microbiome: How urbanization impact coastal microbiomes, as well as novel organisms from Baltic Sea sediment, and deep-sea hydrothermal vents.

Events and jobs

Clinical Lab Technical Asst Sr – Scripps Health – San Diego CA

Postdoctoral Associate in Soil Health and Water Quality – Stroud Water Research Center – Southeast Pennsylvania

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Human oral microbiome

Review: Salivary biomarkers for oral cancer and pre-cancer screening: a review – J Kaur – Clinical Oral Investigations

Review: In Sickness and in Health—What Does the Oral Microbiome Mean to Us? An Ecological Perspective – P.D. Marsh – Advanced in Dental Research

Therapeutic Strategies Targeting Cariogenic Biofilm Microenvironment – Y. Liu – Advanced in Dental Reserach

Human vaginal microbiome

Review: Probiotics in the Prevention and Treatment of Postmenopausal Vaginal Infections: Review Article – Jun-Mo Kim – Journal of Menopausal Medicine

*Associations between sexual habits, menstrual hygiene practices, demographics and the vaginal microbiome as revealed by Bayesian network analysis – Noelle Noyes – PLOSone

Human gut microbiome

Review: Microbiota-Regulated Outcomes of Human Cancer Immunotherapy via the PD-1/PD-L1 Axis – Jaymin Patel – Biochemistry

Review: Microbiome: Gut microbiota sways response to cancer immunotherapy – Ashley York – Nature Reviews Microbiology

Review: Bacterial Signaling at the Intestinal Epithelial Interface in Inflammation and Cancer – Olivia I. Coleman

Characterization of Fusobacterium varium Fv113-g1 isolated from a patient with ulcerative colitis based on complete genome sequence and transcriptome analysis – Tsuyoshi Sekizuka – PLOSone

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Animal experiments

*Diet-induced obesity alters the maternal metabolome and early placenta transcriptome and decreases placenta vascularity in the mouse – Tami J Stuart – Biology of Reproduction

Gastrointestinal Tract Pathology in a BALB/c Niemann–Pick Disease Type C1 Null Mouse Model – Antony Cougnoux – Digestive Diseases and Sciences

Probiotic/prebiotic correction for adverse effects of iron fortification on intestinal resistance to Salmonella infection in weaning mice  – Feifei Lin – Food and Function

Beneficial effects of consumption of acerola, cashew or guava processing by-products on intestinal health and lipid metabolism in dyslipidaemic female Wistar rats – Kamila Sabino Batista – British Journal of Nutrition

*Neisseria gonorrhoeae co-infection exacerbates vaginal HIV shedding without affecting systemic viral loads in human CD34+ engrafted mice – Stacey X. Xu – PLOSone

Plant, root, and soil microbiome

Interspecific plant interactions reflected in soil bacterial community structure and nitrogen cycling in primary succession – Joseph E. Knelman – Frontiers in Microbiology

Analysis of the succession of structure of the bacteria community in soil from long-term continuous cotton cropping in Xinjiang using high-throughput sequencing – Zhang Wei – Archives of Microbiology

Rhizosphere competence and biocontrol effect of Pseudomonas sp. RU47 independent from plant species and soil type at the field scale – Susanne Schreiter – Frontiers in Microbiology

Estimation of throughfall and stemflow bacterial flux in a subtropical oak-cedar forest – Thais B. Bittar – Geophysical Research Letters

NGS of virus-derived small RNAs as a diagnostic method used to determine viromes of Hungarian vineyards – Nikoletta Czotter – Frontiers in Microbiology

Microbial Remediation of Heavy Metals and Arsenic-Contaminated Environments in the Arid Zone of Northwest China – Xiangliang Pan – In: Luo Y., Tu C. (eds) Twenty Years of Research and Development on Soil Pollution and Remediation in China. Springer, Singapore

Review: Induction of abiotic stress tolerance in plants by endophytic microbes – Rusi Lata – Letters in Applied Microbiology

Amendment of Agricultural Soil with Metal Nanoparticles: Effects on Soil Enzyme Activity and Microbial Community Composition – Bahareh Asadishad – Environmental Science and Technology

Water and extremophile microbiome

*Labilibaculum manganireducens gen. nov., sp. nov. and Labilibaculum filiforme sp. nov., Novel Bacteroidetes Isolated from Subsurface Sediments of the Baltic Sea – Verona Vandieken – Frontiers in Microbiology

*Coastal urbanisation affects microbial communities on a dominant marine holobiont – Ezequiel M. Marzinelli – npj Biofilms and Microbiomes

Microbial Communities and Diversities in Mudflat Sediments Analyzed Using a Modified Metatranscriptomic Method – Yong-Wei Yan – Frontiers in Microbiology

*Novel hydrogenases from deep-sea hydrothermal vent metagenomes identified by a recently developed activity-based screen – Nicole Adam – The ISME Journal

The molecular ecology of Microcystis sp. blooms in the San Francisco Estuary – Timothy G. Otten – Environmental Microbiology

Built environment

Dissertation: Developing Quantitative Abundance Metrics for Microbial Communities – Gabriel Goodney – San Diego State University

Resistome

Antibiotic resistance mutations induced in growing cells of Bacillus-related thermophiles – Hirokazu Suzuki – The Journal of Antibiotics

Food microbiology

A metabolomics study reveals enhanced inhibition and metabolic dysregulation in E. coli induced by Lactobacillus acidophilus fermented black tea extract – Kundi Yang – Journal of Agricultural and Food Chemistry

More Microbes

Environmental Sequencing Fills the Gap Between Parasitic Haplosporidians and Free-living Giant Amoebae – Georgia M. Ward – Eukaryotic Microbiology

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Phages and viruses

Rolling-circle replication initiation protein of haloarchaeal sphaerolipovirus SNJ1 is homologous to bacterial transposases of the IS91 family insertion sequences – Yuchen Wang – Journal of General Virology

Preprint: Comparative transcriptomics reveals a conserved Bacterial Adaptive Phage Response (BAPR) to viral predation – Bob G. Blasdel – BioRxiv

Bioinformatics

Phylogeny-Based Kernels with Application to Microbiome Association Studies – Jian Xiao – New Advances in Statistics and Data Science

Techniques

Advantages of meta-total RNA sequencing (MeTRS) over shotgun metagenomics and amplicon-based sequencing in the profiling of complex microbial communities – Fabien Cottier – npj Biofilms and Microbiomes

Ecological Stability Properties of Microbial Communities Assessed by Flow Cytometry – Zishu Liu – mSphere

Deconvolution models for a better understanding of natural microbial communities enumerated by flow-cytometry – Gianluca Corno – Cytometry

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Microbes in the news

Bacteria could cause women to give birth prematurely, study finds – Sabrina Barr – Independent

PCOS may reduce gut bacteria diversity – EurekAlert!

Root microbiome valuable key to plants surviving drought – Elaine Smith – Phys.org

Studies in Mice Suggest How Dietary Fiber Reduces Harmful Effects of High-Fat Diet – Genetic Engineering and Biotechnology News

Helicobacter pylori infection permanently changes gastric environment – Medical Press

Dietary Fiber Intake Protects against Diet-Induced Obesity and Metabolic Syndrome – SCI News

The Microbiome of an Oil Reservoir – UC San Diego

Mucin Cross-Feeding Shapes The Metabolic Environment In The Infant Gut – Vera Bunesova – Science Trends

An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression – Yufeng Qin – Genome Biology

 

January 15, 2018

Today’s digest is full of great papers, including new methods of detection and quantificaion of HGT in anoxic conditions, and a brilliant paper on root-rhizosphere interactome.

General Microbiome

Impact of the start-up process on the microbial communities in biocathodes for electrosynthesis. Mateos, R. Bioelectrochemistry.

Gut Microbiome

Dietary Factors Modulate Colonic Tumorigenesis Through the Interaction of Gut Microbiota and Host Chloride Channels. Zhang Y. Molecular Nutrition Food Research

Metagenomic and metabolomic analyses unveil dysbiosis of gut microbiota in chronic heart failure patients. Cui, X. Scientific Reports

Nasal Microbiome

An insight into intestinal mucosal microbiota disruption after stroke.Stanley,D. Scientific Reports

Influence of pig farming on the human’s nasal microbiota: The key role of the airborne microbial communities. Kraemer, JG. Applied and Environmental Microbiology

Fecal Microbiome

Letters to Editor: Sucrase-isomaltase 15Phe IBS risk variant in relation to dietary carbohydrates and faecal microbiota composition. Thingholm L. Gut

Plant, Soil, and Water Microbiome

Soil contamination alters the willow root and rhizosphere metatranscriptome and the root-rhizosphere interactome. Yergeau, E. The ISME Journal

Indoor Microbiome

Microbiomes in Dishwashers: Analysis of the microbial diversity and putative opportunistic pathogens in dishwasher biofilm communities.Raghupathi, PK. Applied and Environmental Microbiology

Resitome

Characteristics of ARG-carrying plasmidome in the cultivable microbial community from wastewater treatment system under high oxytetracycline concentration. Shi, Y. Applied Microbioloby and Biotechnology

Animan Experiments and Microbiome

Characterizing the bacterial microbiota in different gastrointestinal tract segments of the Bactrian camel. He, J. Scientific Reports

Effect of atorvastatin on the gut microbiota of high fat diet-induced hypercholesterolemic rats. Khan, TJ. Scientific Reports

Protocol/Techniques

Fluorescence recovery allows the implementation of a fluorescence reporter gene platform applicable for the detection and quantification of horizontal gene transfer in anoxic environments. Pinilla, R. Applied and Environmental Microbiology

Microbiome Jobs

Part-Time Microbiology Laboratory Technician

-Inside Higher Ed Careers

January 5, 2018

Today’s digest has an interesting commentary on the oral-gut connection and a brilliant piece on microbial diversity. Lastly, a look at how grapevines influence belowground diversity and networks

General Microbiome

A role for the endometrial microbiome in dysfunctional menstrual bleeding. Pelzer ES. Antonie Van Leeuwenhoek.

Performance and microbial community variations of anaerobic digesters under increasing tetracycline concentrations. Xiong Y. Applied Microbiology and Biotechnology

In Nature, There Is Only Diversity. McLaren MR. MBio.

Gut Microbiome

Commentary: Oral-gut connection: one step closer to an integrated view of the gastrointestinal tract? Lira-Junior R. Mucosal Immunology

Bile acids at the cross-roads of gut microbiome-host cardiometabolic interactions. Ryan PM. Diabeticology and Metabolic Syndrome

REVIEW: Diet, Microbiota, and Metabolic Health: Trade-Off Between Saccharolytic and Proteolytic Fermentation. Korpela K. Annual of Food Science and Technology

Nasal and Lung Microbiome

REVIEW: Fungi in Bronchiectasis: A Concise Review. Máiz L. Internatioanal Journal of Molecular Sciences

Alterations in the mucosa-associated fungal microbiota in patients with ulcerative colitis. Qiu X. Oncotarget

The association between anterior nares and nasopharyngeal microbiota in infants hospitalized for bronchiolitis. Luna PN. Microbiome

Fecal Microbiome

Editorial Comment: Fecal microbiota transplantation as a possible treatment of irritable bowel syndrome. Juncadella AC. Annals of Translational Medicine

Plant, Soil, and Water Microbiome

Co-variation between Distribution of Microbial Communities and Biological Metabolization of Organics in Urban Sewer Systems. Jin P. Environmental Science and Technology.

Do invasive plants structure microbial communities to accelerate decomposition in intermountain grasslands? McTee MR. Ecology and Evolution

Grapevine rootstocks shape underground bacterial microbiome and networking but not potential functionality. Marasco R. Microbiome

Biodiversity of the microbial mat of the Garga hot spring. Rozanov AS. BMC Evolutionary Biology

Animal Experiments and Microbiome

Microbiota Reconstitution Does Not Cause Bone Loss in Germ-Free Mice. Quach D. mSphere

Physiological Translocation of Lactic Acid Bacteria during Pregnancy Contributes to the Composition of the Milk Microbiota in Mice. de Andrés J. Nutrients

Extreme sensitivity to ultraviolet light in the fungal pathogen causing white-nose syndrome of bats. Palmer JM. Nature Communication

OCCURRENCE OF PASTEURELLACEAE BACTERIA IN THE ORAL CAVITY OF SELECTED MARSUPIAL SPECIES. Hansen MJ. Journal of Zoo and Wildlife Medicine

Marine Microbiome

Agelas Wasting Syndrome Alters Prokaryotic Symbiont Communities of the Caribbean Brown Tube Sponge, Agelas tubulata.Deignan LK. Microbial Ecology

Environmental drivers of heterogeneity in the trophic-functional structure of protozoan communities during an annual cycle in a coastal ecosystem. Xu G. Marine Pollution Bulletin

Antibiotic Resitance

Editorial: Empiric antibiotic use in allogeneic hematopoietic cell transplantation: should we avoid anaerobe coverage? Shono Y. Blood Advances

Characterization of genetic determinants involved in antibiotic resistance in Aeromonas spp. and fecal coliforms isolated from different aquatic environments. Carnelli A. Research in Microbiology

 

 

December 11, 2017

Today’s digest is quiet a treat- A microbiome survey of emergency medical service personnel (EMS), a Python release of Mothur, and a global recall of baby formula over contamination scares ( Lactalis )

General Microbiome

 The Emergency Medical Service Microbiome. Hudson AJ. Applied Environmental Microbiology

 Human Gut Microbiome

Towards utilization of the human genome and microbiome for personalized nutrition. Bashiardes S. Current Opinions in Biotechnology

Gut microbial profile analysis by MiSeq sequencing of pancreatic carcinoma patients in China. Ren Z. Oncotarget.

Lung Microbiome

The distal airway microbiome after lung transplantation: A driver of immune regulation? Mitchell AB. Journal of Heart and Lung Transplant

Plant, water, and soil microbiome

 Microbial communities in natural rubber coagula during maturation: impacts on technological properties of dry natural rubber. Salomez M. Journal of Applied Microbiology

Microbial ecology of the Agaricus bisporus mushroom cropping process.McGee CF. Applied Microbiology and Biotechnology

A new niche for anoxygenic phototrophs as endoliths. Roush D. Applied Environmental Microbiology

Animal experiments and microbiome

Co-occurrence of early gut colonization in neonatal piglets with microbiota in the maternal and surrounding delivery environments.Chen X. Anaerobe.

Techniques/Protocol

Metabolic Model Reconstruction and Analysis of an Artificial Microbial Ecosystem. Ye C. Methods in Molecular Biology

mothur-py 0.3.0

-PyPI

Microbes in the NEWS

‘Extremophile’ Antarctic Bacteria Could Unlock Secret to Alien Life (VIDEO)

-Sputnik International

French baby-milk maker Lactalis orders major product recall over bacteria fears

-Prothom Alo (English)

 

 

 

November 30, 2017

A wide variety of interesting articles: Antibiotics administrated during labour impact  infant gut microbiome development, altered gut microbiome is related to liver function in individuals with Hep B, specific pathogens can alter social signaling in drosophila, a comphrensive study of the impact of diet on the lemur gut microbiome, a survey of antibiotic resistence genes in the drinking water across multiple continents, the impact of the hospital microbiome on the gut microbiome of preterm infants, the first evidence of a gut archeae impact on the host immune system, and two popular news articles refuting yesterday’s report of possible alien bacteria on the international space station.

Events and jobs

Web Developer, Microbiome Core – Harvard T.H. Chan School of Public Health

Account Manager – Microbiology –  South East England

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General microbiome

  • Health Economics and Regulations 

Faecal microbiota transplantation: a regulatory hurdle? – Frederick Verbeke – BMC Gastroenterology

Cost-effectiveness analysis of fecal microbiota transplantation for inflammatory bowel disease – Ting Zhang – Oncotarget

Pregnancy and early life

*Intrapartum antibiotics for GBS prophylaxis alter colonization patterns in the early infant gut microbiome of low risk infants – Jennifer C. Stearns – Scientific Reports

Human skin microbiome

Skin Immune Landscape: Inside and Outside the Organism – Florence Abdallah – Mediators of Inflammation

Human gut microbiome
*Gut Microbial Dysbiosis Is Associated with Altered Hepatic Functions and Serum Metabolites in Chronic Hepatitis B Patients – Jing Wang – Frontiers in Microbiology

Faecal bacterial microbiota in patients with cirrhosis and the effect of lactulose administration – Aditya Narayan Sarangi – BMC Gastroenterology

Delivered Fecal Microbiota Transplantation on Recurrent Clostridium difficile Infection – Dina Kao – JAMA

Capsules for Fecal Microbiota Transplantation in Recurrent Clostridium difficile Infection – Krishna Rao – JAMA

Review: Antibiotic therapy in neonates and impact on gut microbiota and antibiotic resistance development: a systematic review – Jon Widding Fjalstad – Journal of Antimicrobial Chemotherapy

Long-term proton pump inhibitor therapy leads to small bowel bacterial overgrowth as determined by breath hydrogen and methane excretion – Agnieszka Sieczkowska – Journal of Breath Research

Review: Impact of gut microbiota on drug metabolism: an update for safe and effective use of drugs – Keumhan Noh – Archives of Pharmacal Research

Evaluating the effect of Clostridium difficile conditioned medium on fecal microbiota community structure – Sabina Horvat – Scientific Reports

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Animal experiments

Preprint: The Vibrio cholerae Type VI Secretion System Can Modulate Host Intestinal Mechanics to Displace Commensal Gut Bacteria – Savannah L Logan – bioRxiv

Genes and Gut Bacteria Involved in Luminal Butyrate Reduction Caused by Diet and Loperamide – Nakwon Hwang – Genes

Simultaneous delivery of antibiotics neomycin and ampicillin in drinking water inhibits fermentation of resistant starch in rats – Diana G. Carvajal-Aldaz – Molecular Nutrition and Food Research

Animal microbiome

*Pathogenic bacteria enhance dispersal through alteration of Drosophila social communication – Ian W. Keesey – Nature Communications

*Feeding strategy shapes gut metagenomic enrichment and functional specialization in captive lemurs – E. A. McKenney – Gut Microbes

Impact of Dietary Galacto-Oligosaccharide (GOS) on Chicken’s Gut Microbiota, Mucosal Gene Expression, and Salmonella Colonization – Rebecca-Ayme Hughes – Frontiers in Veterinary Science

Dietary energy drives the dynamic response of bovine rumen viral communities – Christopher L. Anderson – Microbiome

Effect of microalgae on intestinal inflammation triggered by soybean meal and bacterial infection in zebrafish – Karina Bravo-Tello – PLOS ONE

In vivo effects of Allium cepa L. on the selected gut microflora and intestinal histomorphology in broiler – Sajidur Rahman – Acta Histochemica

Enteric Pathogens and Their Toxin-Induced Disruption of the Intestinal Barrier through Alteration of Tight Junctions in Chickens – Wageha A. Awad – Toxins

Plant, root, and soil microbiome

The Ecological Role of Volatile and Soluble Secondary Metabolites Produced by Soil Bacteria – Olaf Tyc – Trends in Microbiology

Impact of peat mining, and restoration on methane turnover potentials and methane-cycling microorganisms in a northern bog – Max Reumer – Applied and Environmental Microbiology

Burkholderia humptydooensis sp. nov., a New Species Related to Burkholderia thailandensis and the Fifth Member of the Burkholderia pseudomallei Complex – Apichai Tuanyok – Applied and Environment Microbiology

Water and extremophile microbiome
Functional Characterization of Probiotic Potential of Novel Pigmented Bacterial Strains for Aquaculture Applications – Sekar Jinendiran – Probiotics and Antimicrobial Proteins

Resistome

Preprint: Increased usage of antiseptics is associated with reduced susceptibility in clinical isolates of S. aureus – Katherine Hardy – bioRxiv

*Catalogue of antibiotic resistome and host-tracking in drinking water deciphered by a large scale survey – Liping Ma – Microbiome

Review: Assessing the Risk of Antibiotic Resistance Transmission from the Environment to Humans: Non-Direct Proportionality between Abundance and Risk – Célia M. Manaia – Trends in Microbiology

Built environment

*Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome – Brandon Brooks – Nature Communications

Predominance and Metabolic Potential of Halanaerobium spp. in Produced Water from Hydraulically Fractured Marcellus Shale Wells – Daniel Lipus – Applied and Environment Microbiology

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Microbial Ecology

Effect of Antimicrobial and Physical Treatments on Growth of Multispecies Staphylococcal Biofilms – Elizabeth J. Stewart – Applied and Environment Microbiology

More Microbes

  • Archaea

*Associated Archaeon Methanosphaera stadtmanae Is Recognized through Its RNA and Induces – Tim Vierbuchen – Frontiers in Immunology

  • Synthetic Microbes

Analysis and Implementation of a Multicellular Feedback Control Strategy in a Synthetic Bacterial Consortium – Gianfranco Fiore – ACS Synthetic Biology

Techniques

Diazotroph community characterization via a high-throughput nifH amplicon sequencing and analysis pipeline – John Christian Gaby – Applied and Environmental Microbiology

Direct PCR Offers a Fast and Reliable Alternative to Conventional DNA Isolation Methods for Gut Microbiomes – Elin Videvall – mSystems

Generation of bacteriophage-insensitive mutants of Streptococcus thermophilus using an antisense RNA CRISPR-Cas silencing approach – Brian McDonnell – Applied and Environmental Microbiology

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Microbes in the news

*Bacteria on Space Station Likely From Germy Humans, Not Aliens – Elaina Zachos – National Geographic

*We are basically positive that the Russians did not find alien bacteria in space – Mary Beth Griggs – Popular Science

Custom Bacteria Make New Molecules On Demand – Sam Lemonick – Forbes

Toilet art sheds light on gut health – Newshub

November 28, 2017

Identification of nitrite-oxidizing bacteria important for dark ocean carbon fixation, effects of antibiotic exposure to the maternal gut microbiota extend to offspring in mice and enhance colitis, a review on genome mining for natural products discovery.

Events and jobs

Postdoc position on biofilm-mediated co-evolution of industrial strains – Biologisk Institut, University of Copenhagen, Denmark

Human skin microbiome

Measuring the microbiome of chronic wounds with use of a topical antimicrobial dressing – A feasibility study – Lindsay Kalan – PLOS ONE

Human gut microbiome

Pre-print: Endospores and other lysis-resistant bacteria comprise a widely shared core community within the human microbiota – Sean M Kearney – bioRxiv

Opinion: Human Gut Microbiome: Function Matters – Anna Heintz-Buschart – Trends in Microbiology

Review: The gut microbiome, symptoms, and targeted interventions in children with cancer: a systematic review – Jinbing Bai – Supportive Care in Cancer

Animal experiments

Intergenerational transfer of antibiotic-perturbed microbiota enhances colitis in susceptible mice – Anjelique F Schulfer – Nature Microbiology

Canagliflozin reduces plasma uremic toxins and alters the intestinal microbiota composition in a chronic kidney disease mouse model – Eikan Mishima – American Journal of Physiology, Renal Physiology

Insect-based diet, a promising nutritional source, modulates gut microbiota composition and SCFAs production in laying hens – Luca Borrelli – Scientific Reports

Animal microbiome

Comparison of the gut microbiota composition between wild and captive sika deer (Cervus nippon hortulorum) from feces by high-throughput sequencing – Yu Guan – AMB Express

Plant, root, and soil microbiome

Pre-print: The effects of host species and sexual dimorphism differ among root, leaf and flower microbiomes of wild strawberries in situ – Na Wei – bioRxiv

Water and extremophile microbiome

Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation – Maria G Pachiadaki – Science

Investigating the bacterial community and amoebae population in rural domestic wastewater reclamation for irrigation – Bingjian Cui – Journal of Environmental Sciences

Phages and viruses

Review: Viruses of archaea: Structural, functional, environmental and evolutionary genomics – Mart Krupovic – Virus Research

Bioinformatics

Review: Omics-based natural product discovery and the lexicon of genome mining – Henrique Machado – Current Opinion in Microbiology

More microbes

Chromosome level assembly and secondary metabolite potential of the parasitic fungus Cordyceps militaris – Glenna J Kramer – BMC Genomics

Genomic assessment in Lactobacillus plantarum links the butyrogenic pathway with glutamine metabolism – Cristian Botta – Scientific Reports

Microbes in the news

Researchers conduct novel wheat microbiome analysis under four management strategies – Phys.Org

Fertility clinics treat abnormal vaginal bacteria aiming to improve reproductive outcome – Medical Xpress

Microbe threat to Mars – Andrew Masterson – Cosmos

Flies’ Feet Can Spread Bacteria – Kerry Grens – The Scientist

Despite Their Tiny Genome, A Beetle’s Bacteria Pack A Big Punch – Julianna LeMieux – American Council on Science and Health

CRISPR Harnessed to Turn Bacteria into Microscopic Tape Recorders – Genetic Engineering & Biotechnology News

Bacteria hysteria

Warning: Those lipstick samples could be loaded with poop, investigation finds – Mandy Matney – Sacramento Bee

Science, career, and publishing

Pre-print: A design framework and exemplar metrics for FAIRness – Mark D Wilkinson – bioRxiv